I'm sorry I can't help further. It works fine on my system. Maybe someone else can comment.<br><br>Bill<br><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 4:05 PM, Sarah Waldron <span dir="ltr"><<a href="mailto:sarah.waldron11@yahoo.com">sarah.waldron11@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Yes I pressed "c" then changed the directory for ITK when it gave me an error. Then I pressed "g". Then I typed make in the terminal and got this error although a make file did become created in the folder. <br>
<div class="im"><br>--- On <b>Mon, 11/16/09, Bill Lorensen <i><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></i></b> wrote:<br></div><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<div class="im"><br>From: Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>><br>Subject: Re: [Insight-users] image preprocessing<br>To: "Sarah Waldron" <<a href="mailto:sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>><br>
Cc: "Luis Ibanez" <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>>, <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br></div>Date: Monday, November 16, 2009, 8:45 PM<div>
<div></div><div class="h5"><br><br><div>When you run ccmake, I assume you configure and generate? Are there errors reported?<br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 3:26 PM,
Sarah Waldron <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
<div>Ok I did what you said, and I set the ITK-directory. But it is still not building. Here's the terminal output:<br><br>sarah@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/<br>
<br><br>sarah@sarah-laptop:~$ make<br>make: *** No targets specified and no makefile found. Stop.<br><br></div>--- On <b>Mon, 11/16/09, Bill Lorensen <i><<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></i></b> wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Bill Lorensen <<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>><div>
<br>Subject: Re: [Insight-users] image preprocessing<br>To: "Sarah Waldron" <<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>><br></div>
<div>Cc: "Luis Ibanez" <<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>>, <a rel="nofollow" href="http://mc/compose?to=insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
Date: Monday, November 16, 2009, 6:26 PM<br><br></div><div><div></div><div><div>Sarah,<br><br>Try this:<br><br>ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true ../InsightApplications//MRIBiasCorrection/<br>
<br>where ../InsightApplications//MRIBiasCorrection/ points to your source.<br><br>Then, you will need to define ITK_DIR during the configure process.<br>
<br>Bill<br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 1:09 PM, Bill Lorensen <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sarah,<br><br>Sorry, I just tried my suggestion and I get the same errors. I do not see an ITK_DIR in my cache.<br><font color="#888888"><br>Bill</font><div><div></div><div><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 1:00 PM, Bill Lorensen <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">When you ran ccmake did you specify ITK_DIR to tell the app where to find itk's build?<div>
<div></div><div><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 12:22 PM, Sarah Waldron <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo..com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
I tried to build the files in<br>
InsightApplications/MRIBiasCorrection<br>
by typing:<br>
<br>
ccmake . <br>
make<br>
<br>
but I get all these errors:<br>
<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .<br>
<br>
<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ make<br>
Scanning dependencies of target BiasCorrector<br>
[ 6%] Building CXX object CMakeFiles/BiasCorrector.dir/BiasCorrector.o<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector..cxx:19:26:
error: vnl/vnl_math.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:20:28: error: itkWin32Header.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:25:22: error: itkArray.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:24:45:
error: itkMRIBiasFieldCorrectionFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:25:46:
error: itkMinimumMaximumImageCalculator.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector..cxx:26:43:
error: itkBinaryThresholdImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:27:36:
error: itkImageRegionIterator.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:28:58:
error: itkZeroCrossingBasedEdgeDetectionImageFilter.h: No such file or
directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:29:45:
error: itkBinaryBallStructuringElement.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:30:46:
error: itkBinaryCrossStructuringElement..h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:31:40:
error: itkBinaryDilateImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10..0/MRIBiasCorrection/BiasCorrector.cxx:32:32:
error: itkMaskImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:33:32:
error: itkCastImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:34:23: error: itkIndent.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:35:26:
error: itkHistogram.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:20:32:
error: itkExceptionObject.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:21:35:
error: itkMetaImageIOFactory.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:22:32:
error: itkImageFileReader.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils..h:23:32:
error: itkImageFileWriter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:25:45:
error: itkImageRegionIteratorWithIndex.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:26:30:
error: itkNumericTraits.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:27:34:
error: itkOrientImageFilter.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,<br>
from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:20:28: error: vnl/vnl_vector.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: ‘itk’ has not been declared<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: expected ‘,’ or ‘...’ before ‘<’ token<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,<br>
from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: variable or field ‘dump’ declared void<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: ‘vnl_vector’ was not declared in this scope<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: expected primary-expression before ‘double’<br>
make[2]: *** [CMakeFiles/BiasCorrector.dir/BiasCorrector.o] Error 1<br>
make[1]: *** [CMakeFiles/BiasCorrector.dir/all] Error 2<br>
make: *** [all] Error 2<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ <br>
<br>
Can someone tell me what's wrong.<br>
Sarah.<br><br>--- On <b>Thu, 11/5/09, Luis Ibanez <i><<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<br>From: Luis Ibanez <<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>><br>Subject: Re: [Insight-users] image preprocessing<br>To: "Sarah Waldron" <<a rel="nofollow" href="http://mc/compose?to=sarah..waldron11@yahoo.com" target="_blank">sarah..waldron11@yahoo.com</a>><br>
Cc: <a rel="nofollow" href="http://mc/compose?to=insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>Date: Thursday, November 5, 2009, 2:29 AM<div><div></div><div><br><br><div><br>Hi Sarah,<br><br>You may want to try the same filters that are used for correcting <br>
for MRI intensity inhomogeneity.<br><br>See the directory:<br>InsightApplications/MRIBiasCorrection<br><br>These classes approximate the illumination distribution with a <br>
polynomial, and then use the polynomial in order to normalize<br>the intensity across space.<br><br>You may also find useful the following paper of the Insight Journal:<br><br>"N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction"<div>
Tustison N., Gee J.</div>
<div>PICSL, University of Pennsylvania<br><br></div><a rel="nofollow" href="http://www.insight-journal.org/browse/publication/640" target="_blank">http://www.insight-journal.org/browse/publication/640</a><br><br><a rel="nofollow" href="http://hdl.handle.net/10380/3053" target="_blank">http://hdl.handle.net/10380/3053</a><br>
<br><br><br> Regards,<br><br><br> Luis<br><br><br>----------------------------------------------------------------------------<br><div class="gmail_quote">On Wed, Nov 4, 2009 at 5:28 PM, Sarah Waldron <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
<div>Hi,</div>
<div>I'm new to ITK. I have a series of brain images taken with a camera that when combined are supposed to form a 3 dimensional volume. The camera had a flash and the slices don't all have the same lighting and shadowing effects. Does anyone have any suggestions how to correct this so that all the images have the same light distribution?</div>
<div>Thanks,</div>
<div>Sarah</div></td></tr></tbody></table><font color="#888888"><br>
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